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PubMed1997

Calibration and storage of DNA competitors used for contamination-protected competitive PCR.

DNA fragments used as standards in competitive PCR were precisely calibrated using HPLC and commercially available DNA molecular mass markers. The accuracy of calibration was reflected by data that differed by only 2% from the mean when two independently purified and calibrated competitor preparations were compared. Highly dilute competitor solutions were stable at -20 degrees C for up to 1 year in the presence of carrier HindIII-digested lambda DNA, but progressive loss of competitor DNA with increasing storage time was observed when carrier DNA was omitted from the solution. Applying 0.2 U uracil-DNA glycosylase (UDG) per assay of remaining temperature-stable activity did not effect the ratios of synthesized products. This study describes quality management in PCR quantitation that is useful for the measurement of multidrug resistance-associated protein (MRP) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene transcripts.

ATP-Binding Cassette Transporters↗
PubMed2001

Polychlorinated biphenyl contamination and minisatellite DNA mutation rates of tree swallows.

The evidence that exposure to polychlorinated biphenyls (PCBs) leads to mutations is equivocal and controversial. Using multilocus DNA fingerprinting, we compared the mutation rate of tree swallows (Tachycineta bicolor) nesting at sites with high and low levels of contamination with PCBs. The upper Hudson River, USA, is highly contaminated with PCBs as a result of releases from two capacitor manufacturing plants in Hudson Falls and Fort Edward, New York, USA. Tree swallows nesting nearby have some of the highest known concentrations of PCBs in their tissues of any contemporary bird population (up to 114,000 ng PCB/g tissue). We found no difference in mutation rates between sites in New York with high PCB contamination and reference sites in Wisconsin, USA, and Ontario and Alberta, Canada, with known or presumably low levels of contamination. Thus, the mechanism behind altered reproductive behavior of tree swallows along the upper Hudson River is most likely physiological impairment, such as endocrine disruption, rather than mutation.

Animals↗
PubMed1994

Detection of HER-2/neu oncogene amplification in flow cytometry-sorted breast ductal cells by competitive polymerase chain reaction.

BACKGROUND: The amplification and/or overexpression of the HER-2/neu oncogene has been proposed as an important prognostic marker in breast cancer. However, contradictory results from various groups regarding whether there is statistical significance in HER-2 amplification or overexpression in predicting overall and disease free survival in node positive versus node negative patients exist in the literature. Current assays on quantifying the HER-2 oncogene rely on DNA extracted from homogenized breast tissue. Not only is a large amount of tissue required, but also, the DNA extract is contaminated with DNA from stromal cells and leukocytes, leading to decreased specificity and sensitivity of the HER-2 assay. Improving the specificity (DNA from breast ductal cells) and the sensitivity (competitive polymerase chain reaction [PCR]) of the HER-2 amplification detection assay will help resolve some of these controversies. METHODS: Using multiparameter flow cytometry (FCM), ductal cells from breast biopsies and fine needle aspirations (FNAs) are identified and selectively sorted using anti-cytokeratin, anti-HER-2 antibody labeling and DNA staining. HER-2 amplification in these sorted cells is then quantified by competitive DNA PCR using a competitive reference standard mutant template that is susceptible to the restriction enzyme Sma-1. RESULTS: Applying this strategy, SK-BR-3, an HER-2 amplified breast cancer cell line, was found to have approximately 9x baseline HER-2 oncogene copies. In addition, MCF-7, a known HER-2 nonamplified breast cancer cell line, was found to have baseline HER-2 oncogene copies. In the 10 clinical breast samples tested, 4 of the 10 breast cancers were HER-2 amplified using as few as 1000 cells. The cytokeratin positive cells of these cancers, in contrast to the cytokeratin negative cells, have detectably higher HER-2 amplification (7.2 +/- 2.8x versus 3.2 +/- 1.1x, respectively). Hence, HER-2 gene amplification would have been underestimated if unsorted cells were used because of stromal dilution. In the cytokeratin positive cells that were HER-2 oncogene amplified, corresponding HER-2 oncoprotein overexpression was detected by FCM. CONCLUSIONS: Using FCM, the ductal cell subpopulation of a breast specimen can be successfully sorted from breast biopsy and FNA specimens. Moreover, by applying the technique of competitive PCR, improved specificity and sensitivity in HER-2 oncogene amplification detection is achieved. The entire procedure can be accomplished in 1 day, allowing for a cost-effective assay and rapid turnaround time.

Base Sequence↗
PubMed2003

DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones.

We have designed DOP-PCR primers specifically for the amplification of large insert clones for use in the construction of DNA microarrays. A bioinformatic approach was used to construct primers that were efficient in the general amplification of human DNA but were poor at amplifying E. coli DNA, a common contaminant of DNA preparations from large insert clones. We chose the three most selective primers for use in printing DNA microarrays. DNA combined from the amplification of large insert clones by use of these three primers and spotted onto glass slides showed more than a sixfold increase in the human to E. coli hybridization ratio when compared to the standard DOP-PCR primer, 6MW. The microarrays reproducibly delineated previously characterized gains and deletions in a cancer cell line and identified a small gain not detected by use of conventional CGH. We also describe a method for the bulk testing of the hybridization characteristics of chromosome-specific clones spotted on microarrays by use of DNA amplified from flow-sorted chromosomes. Finally, we describe a set of clones selected from the publicly available Golden Path of the human genome at 1-Mb intervals and a view in the Ensembl genome browser from which data required for the use of these clones in array CGH and other experiments can be downloaded across the Internet.

Animals↗
PubMed2001

HIV DNA integration during cell-to-cell transmission of infection: evidence for partially integrated DNA structures in acutely infected cells.

A one-step cell-to-cell transmission model of human immunodeficiency virus (HIV) infection was used to study viral DNA integration in the early phase of viral replication. Co-culturing H3B cells as virus donors with CD4+ Hut78 recipient cells in a ratio of 1:4 produced a synchronous, one-step viral infection with de novo synthesis of unintegrated HIV DNA within 4 h p.i., which subsequently integrates in the host genomic DNA to form provirus. To study the kinetics of viral DNA integration, cellular chromosomal DNA was isolated at different times after co-culturing and extensive electrophoresis was used to remove residual unintegrated viral DNA. Removal of contaminating, unintegrated viral DNA in the purified chromosomal DNA fraction was confirmed by various experiments. When purified chromosomal DNA (free of contaminating unintegrated viral DNA)--from the mix of acutely infected cells--was digested with restriction enzymes KpnI, BamHI or PstI and analysed by Southern blot hybridization, integration of viral DNA into chromosomal DNA was first observed at 8 h p.i. and was essentially complete by 72 h p.i. In addition, evidence was found for a relatively stable, partially integrated HIV DNA structure within the chromosomal DNA, that was first detectable at 8 h p.i. and did not become fully integrated until 72 hours post infection.

Blotting, Southern↗
PubMed1982

Effect of polyamines on two types of reaction of purified poly(ADP-ribose) polymerase.

The effects of polyamines on reactions catalyzed by bovine thymus poly(ADP-ribose) polymerase were examined under various conditions, and the following results were obtained. (1) Spermine and spermidine, and putrescine to a lesser degree can stimulate the synthesis of poly(ADP-ribose) covalently bound to the enzyme without Mg2+ and histones. (2) A part of the above stimulation can be explained by the Mg2+-sparing effect of polyamines. (3) The other part of the stimulation is shown to be through protection of the enzyme against the formation of an abortive complex of the enzyme and denatured DNA, which contaminates some native DNA preparations used for enzyme activation. Similar protection was shown earlier in this laboratory with histones. (4) Putrescine seems to lack this enzyme-protecting activity. (5) The polyamine effect observed in the Mg2+-dependent reaction is variable depending on the DNA preparations used. (6) Chemical analysis shows that the average chain lengths of the products synthesized with Mg2+ and spermine are similar, and the products are covalently bound to the enzyme, indicating that the reaction supported by polyamines is essentially the same as that by Mg2+. (7) Under the histone H1-dependent reaction conditions where ADP-ribosylation of histone H1 is predominant, both Mg2+ and polyamines are inhibitory on the reaction and both cations decrease the number of product molecules without affecting the size of the product. These data suggest that polyamines can at least partially replace Mg2+ in terms of effect on the ADP-ribosylation reaction. The other effect of polyamines is the protection of the enzyme from abortive binding to denatured DNA, as has also been shown to occur with histones.

Animals↗
PubMed1991

RNA polymerase II elongation complexes paused after the synthesis of 15- or 35-base transcripts have different structures.

We have purified specific RNA polymerase II elongation intermediates initiated at the adenovirus type 2 major late promoter and paused either 15 or 35 to 36 bases downstream of the transcription initiation site. Transcription was arrested at these two sites by combining modification of the promoter sequence with limitation of appropriate nucleotide concentrations in the in vitro reaction. The resultant complexes were remarkably stable and could be purified away from free DNA and contaminating protein-DNA complexes, without loss of activity, by the use of sucrose gradient sedimentation and low-ionic-strength polyacrylamide gel electrophoresis. The complexes were characterized by both DNase I and o-phenanthroline-copper ion nuclease protection assays. The DNase I footprints revealed that the structures of the 15- and 35- to 36-nucleotide transcription complexes differed from those previously reported for an adenovirus type 2 major late preinitiation complex and a subsequent intermediate formed upon addition of ATP. Furthermore, the 35- to 36-nucleotide complex protected a significantly smaller portion of the template than the 15-nucleotide species and migrated at a slightly higher rate in polyacrylamide gels. These observations suggest that changes in structural organization may continue to occur in transcription complexes which are already committed to elongation.

Base Sequence↗
PubMed2005

Identification of unknown body using DNA analysis and dental characteristics in chest X-ray photograph.

An unknown skeletonized body was identified by DNA analysis and dental information. The body had already been cremated when a candidate for the unknown body was proposed. Therefore, for DNA analysis we used teeth that had been kept for a long time after use for serological examination. We also used a chest X-ray photograph of the candidate and photographs of dentition, as well as dental X-ray photographs taken when the unknown body was found. Because DNA obtained from teeth was highly degraded, we amplified three PCR fragments to determine the 766 bp mitochondrial DNA (mtDNA) sequence including HV1 and HV2. Polymorphism of the ABO locus was also analyzed using small PCR fragments. Although the isolated DNA was contaminated, probably with DNA from a different individual, DNA polymorphisms of mtDNA and the ABO locus could be analyzed. We discuss the reliability of our conclusions from the point of view of the necessity of constructing an accurate mtDNA database. Although a dentist who had treated the teeth of the unknown body could not be found, a chest X-ray photograph for medical diagnosis was very useful in comparing dental characteristics, as it included an image of the frontal part of the lower jaw and upper teeth.

ABO Blood-Group System↗
PubMed1993

Fusion activity dissociated from replication ability in feline immunodeficiency virus (FIV) in human cells.

Multinucleated-giant-cell formation followed by cell killing was observed after cocultivation of the feline immunodeficiency virus (FIV)-producing feline T-cell line 3201/FIV with various human cells, including T-cell lines carrying human T-cell lymphotropic virus type I (HTLV-I). The susceptibility to giant cell formation varied with the cell lines tested. Cocultivation of irradiated 3201/FIV cells with MT-2 cells resulted in giant cell formation as early as 2 h in culture, with striking resemblance to that induced by human immunodeficiency virus (HIV). MT-4 cells (HTLV-I positive) and H9 cells (HTLV-I negative) were less susceptible than MT-2 to the induction of syncytia. MOLT-4 cells (HTLV-I negative) had intermediate sensitivity to syncytia formation. No syncytia were observed in the monocytic cell line U-937 (HTLV-I negative). Syncytia formation between 3201/FIV and MT-2 cells was inhibited by polyclonal cat anti-FIV antisera but not polyclonal cat anti-feline leukemia virus (FeLV) antisera, goat anti-FeLV, uninfected specific-pathogen-free cat serum, human anti-HTLV-I antisera, or normal human and goat serum. Concentrated cell-free FIV supernatant from 3201/FIV also induced giant cells of MT-2 cells that were indistinguishable from those induced by cocultivation. Giant cells and extensive cell killing associated with giant cell formation declined and disappeared within 10 days. Surviving cells appeared to be of normal size and grew continuously without expressing FIV antigen or releasing infective virus. Although Southern blot analysis using probes specific for FIV could not detect proviral DNA in any of the five human cell lines cocultured with irradiated 3201/FIV cells, the polymerase chain reaction (PCR) technique detected FIV-specific DNA in MOLT-4 cells. DNA from the FIV-PCR positive MOLT-4 cells was PCR negative for endogenous FeLV-specific sequences, indicating that the MOLT-4 cell DNA was not contaminated with DNA from feline cells (i.e., 3201 cells). The FIV-MOLT-4 cells remained PCR positive for FIV after 40 passages, suggesting stable integration in the human cell line. These findings indicate that FIV is capable of forming proviral DNA in human T-lymphoid cells by cocultivation, although this FIV-carrying human cell line failed to produce replication-competent viruses.

Animals↗
PubMed1994

Identification and elimination of DNA sequences in Taq DNA polymerase.

This study confirms that different preparations of Taq DNA polymerase are contaminated with eubacterial DNA. The contaminants appeared to represent more than one strain or species but were not identified as Thermus aquaticus or Escherichia coli. Differences in microcentrifuge tube composition appeared to affect elimination of the contaminants.

Base Sequence↗
PubMed2006

Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA.

In this study, we adapted the well known uracil DNA glycosylase (UNG) carry-over prevention system for PCR, and applied it to the analysis of DNA methylation based on sodium bisulfite conversion. As sodium bisulfite treatment converts unmethylated cytosine bases into uracil residues, bisulfite treated DNA is sensitive to UNG treatment. Therefore, UNG cannot be used for carry-over prevention of PCR using bisulfite treated template DNA, as not only contaminating products of previous PCR, but also the actual template will be degraded. We modified the bisulfite treatment procedure and generated DNA containing sulfonated uracil residues. Surprisingly, and in contrast to uracil, 6-sulfonyl uracil containing DNA (SafeBis DNA) is resistant to UNG. We showed that the new procedure removes up to 10,000 copies of contaminating PCR product in a closed PCR vessel without significant loss of analytical or clinical sensitivity of the DNA methylation analysis.

Colonic Neoplasms↗
PubMed1986

Genomic 5-methylcytosine determination by 32P-postlabeling analysis.

A simple and sensitive method for the quantitation of 5-methyldeoxycytidine in DNA has been developed by the adaptation of the Randerath 32P-postlabeling technique. Nucleic acids were digested to 3'-monophosphate nucleotides, which were converted to 32P-labeled 3',5'-bisphosphate nucleotides, the 3'-phosphate was cleaved by the action of nuclease P1, and the resultant 5'-[32P]-monophosphate nucleotides were separated by two-dimensional thin-layer chromatography. Less than 1 microgram of DNA was required for the precise quantitation of 5-methyldeoxycytidine content to a detectable limit of 0.01% of the total cytidine residues methylated. The genomic 5-methyldeoxycytidine content may thus be quantitated in tissue samples, small or selective cell populations, senescing or terminally differentiating cells, or DNA from any source. We report here, for the first time, the genomic 5-methyldeoxycytidine content of normal human bronchial epithelial and normal human pulmonary mesothelial cells. The chromatographic separation of all of the normal and some of the rare monophosphate deoxyribonucleotides and ribonucleotides has been characterized. Thus, 5-bromodeoxyuridine and the RNA contamination of DNA or the DNA contamination of RNA can also be quantitated during the same analysis.

5-Methylcytosine↗